search for: drosophila

Dear all, I am currently analyzing a set of arrays hybe on the lattest affy Drosophila 2.0 GeneChip. I am trying to run simple annaffy analysis but can¹t find what is the name of the annotation file I need to use. Here is the output of the AffyBatch object I am using: > expData AffyBatch object size of arrays=732x732 features (16749 kb) cdf=Drosophila_2 (18952 affyids) number of...

Hello, Please have a look at the code below, which I use to read in the attached file. As line 18 of the file reads "1065:>sp|Q9V3T9|ADRO_DROME NADPH:adrenodoxin oxidoreductase, mitochondrial OS=Drosophila melanogaster GN=dare PE=2 SV=1", I expect the code below to produce a 3 column data frame with most of the last column empty and line 18 to produce a data.frame row like so: V1 1065 V2 >sp|Q9V3T9|ADRO_DROME NADPH V3 adrenodoxin oxidoreductase, mitochondrial OS=Drosophila melanogast...

I am a relative newbie to survival analysis and R in general, but would like to use the coxme package to analyse some data I currently have. The data is relative to survival times of drosophila melanogaster populations to infection with pathogens, and has the variables: Time, Status, Treatment (4 treatments + 2 controls) Population Replicate ?and I'm currently using the following call mixed<- coxme(formula = Surv(Time, Status) ~ strata(Treatment) + (1 | Population/Replicate),x=T,y=...

Dear all, Here is my code which am using to combine 5th column from different data sets. Here is the function to do my job genesymbol.append.file <-NULL gene.column <- NULL readGeneSymbol <- function(files,genesymbol.column=5){ for(i in fnames){ temp <- read.table(fnames,header=T,sep="\t",stringsAsFactors=F,quote="\"")

Hi everybody, I have a problem when trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD AFFX-r2-Ec-bioD-3_at spk creX AFFX...

Dear all, I have a data which is in text file and i would like to import the data to R. From the manual, i?ve found the read.table command function is the most appropriate but when i wrote the command an error had occur. It say ?Error in read.table"C:/Users/user/Documents/cfa-1.txt", header = T, sep = "\t",skip=10) :more columns than column names?. Please help me with this as

I am running R version ??? under Redhat 5.2. It seems as though the --nsize object has no effct on the size of the allocated Ncells as determined using gc(). Yes, I have that much data.... That is if I envoke R with R --vsize 100 --nsize 5000000 then type gc() I get free total Ncells 92202 200000 Vcells 12928414 13107200 Thanks Tony Long Ecology and Evolutionary Biology Steinhaus

...SDh7_cz71dVqiRf1mkMT-Z@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > I am a relative newbie to survival analysis and R in general, but > would like to use the coxme package to analyse some data I currently > have. > The data is relative to survival times of drosophila melanogaster > populations to infection with pathogens, and has the variables: > Time, > Status, > Treatment (4 treatments + 2 controls) > Population > Replicate > ?and I'm currently using the following call > mixed<- coxme(formula = Surv(Time, Status) ~ strata(Treatm...